title: the fourth largest follicle (F4) rep4

description:
domestic goose
4HPGF4


title: Large white follicle rep3

status: Public on Oct 16 2019

type: SRA

city: Chongqing

first: Gao

last: Guangliang

address: Street Address, No. 51 Changlong Avenue Rongchang County

country: China

institute: Chongqing Academy of Animal Sciences

description:
domestic goose
3HPG4-6

library_source: transcriptomic

data_processing:
Illumina CASAVA ver.1.8.2 software was used for basecalling.
We removed low-quality reads including those with ≥ 10% unidentified nucleotides, > 10 nt aligned to the adapter, allowing ≤ 10% mismatches, and with > 50% of bases with phred quality < 5. Then, high-quality reads of six strand-specific libraries were mapped to the pig reference genome (Suscrofa.10.2 from Ensemble) with TopHat (v.2.1.0)
mRNA expression levels of fragments per kilobase per million mapped reads (FPKM) were obtained using Cufflinks (v.2.2.1).
Cuffquant (part of Cufflinks) was used to generate abundance files, which were applied to Cuffdiff (part of Cufflinks) to detect DE mRNAs/genes between the two groups.
Transcripts were assembled by Stringtie version 1.2.2.
AssemblyLine (http://assemblyline.googlecode.com) was used to characterize and filter background noise and to perform meta-assembly by merging the assembled transcripts.
Coffcompare (part of Cufflinks, version 2.2.1) was used to remove transcripts annotated in the reference sequence (marked by ‘c’ for partial match or ‘=’ for full match).
Each transcript sequence was translated in all six possible frames with Transeq (part of EMBOSS version 6.5.7) and the transcript with translated protein sequences that had a significant hit in the Pfam (release27) database with HMMER (v3.1b2) were excluded.
Remaining transcripts were compared with human and mouse genomes, and the UniRef database with BLASTX, then, potential coding transcripts were removed.
The Coding Potential Calculator (CPC) was used to assess the coding potential of the remaining transcripts.
To obtain genomic characterizations for all identified lncRNA transcripts, we ran FEELnc_classifier.pl (a Perl script in FEELnc).
Genome_build: Goose
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample.

molecule: total RNA

organism: Anser cygnoides

source_name: goose granulosa cells

extract_protocol:
Total RNA was isolated from each sample with Trizol reagent (Life Technologies, Beijing, China) according to the manufacturer's instruction.
Approximately 1 µg total RNA and the Ribo-Zero™ kit (Epicentre, Madison, WI, USA) were used to generate RNA-Seq cDNA libraries from each sample, and then, RNA sequencing was performed following the manufacturer's standard procedures.

tag: development stage

value: LWF

tag: tissue

value: goose granulosa cells

tag: age

value: 40 Week


title: Large white follicle rep2

description:
domestic goose
2HPG4-6


title: Samll white follicle rep3

description:
domestic goose
3HPG2-4

value: SWF


title: Large white follicle rep1

description:
domestic goose
1HPG4-6


title: Samll white follicle rep2

description:
domestic goose
2HPG2-4


title: Large yellow follicle rep5

description:
domestic goose
5HPG8-10

value: LYF


title: Samll white follicle rep1

description:
domestic goose
1HPG2-4


title: PfOO-3

status: Public on Oct 01 2019

city: University Park

first: Scott

middle: E.

last: Lindner

state: Pennsylvania

address: W224 Millennium Science Complex

department: Biochemistry and Molecular Biology

country: USA

institute: Penn State University

data_processing:
Tophat2: each batch of reads was aligned to the reference genome (PY17X v32 or PF3D7 v30)
htseq-count:These reads were then aligned to the annotated transcriptome of P. yoelii (v32 from PlasmoDB) or P. falcipari, (v30 from PlasmoDB) using htseq-count. We utilized the Union method for reads overlapping annotated transcripts.
DESeq2: The count files from htseq-count were merged and compared across conditions using DESeq2.  Samples were grouped and compared between Oocyst sporozoites and salivary gland sporozoites within the same organism. These were compared by the parametric fit type with outlier replacement turned on to normalize variance between the count files.
Genome_build: All data sets were aligned to the PY17X Genome v32 or PF3D7 Genome v30 obtained from PlasmoDB. The same version of the annotated transcriptome was used for the ht-seq count step of the analysis.
Supplementary_files_format_and_content: The processed data file contains the output from the DESeq2 program. These have been combined with the normalized read outputs for each run, as well as supplemented with the means and standard error of the mean for each batch.

organism: Plasmodium falciparum 3D7

source_name: Oocyst Sporozoites

growth_protocol: Plasmodium yoelii or Plasmodium falciparum gametocytes were fed to Anopheles stephensi mosquitoes, and infections were allowed to proceed for 10 days (oocyst sporozoites) or 14 days (salivary gland sporozoites)

extract_protocol:
Cells were lysed and RNA purified using a Qiagen Rneasy Kit with additional DNaseI on-column digestions.
A barcoded library was made from each sample by using the Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, Cat# RS-122-2101) according to the manufacturer's protocol. qPCR was performed to determine the concentration of each library and an equimolar pool was made of all libraries. The library pool was sequenced on an Illumina HiSeq 2500 in Rapid Run mode according to the manufacturer's protocol.
100 nt single read RNA-sequencing

treatment_protocol: Sporozoites were purified twice with sequential Accudenz discontinuous density gradients.

value: Oocyst Sporozoites


title: PfSG-1

source_name: Salivary Gland Sporozoites

value: Salivary Gland Sporozoites


title: PfOO-2


title: PfOO-1


title: PySG-2

organism: Plasmodium yoelii yoelii 17XNL


title: PyOO-1


title: PyOO-3


title: PySG-1


title: PfSG-3


title: PySG-3


title: Samll white follicle rep5

description:
domestic goose
5HPG2-4


title: CC-seq of S. cerevisiae Top2: pdr1, vegetative (YPD), VP16, BioRep1, TechRep1

status: Public on Sep 28 2019

city: Brighton

first: William

last: Gittens

state: I am not in the U.S. or Canada

address: Science Park Road

department: Genome Damage and Stability Centre

country: United Kingdom

institute: University of Sussex

description: CC-seq map of Top2-DNA CCs

library_source: genomic

data_processing:
Paired end reads that passed filter were aligned to Cer3H4L2 (https://github.com/Neale-Lab) using bowtie2 (options: -X 1000 --no-discordant --very-sensitive --mp 5,1 --np 0), using MAPQ0 settings
SAM files processed via terminalMapper (Perl, v5.22.1; https://github.com/Neale-Lab) that computes the coordinates of the protein-linked 5’-terminal nucleotide.
PCR duplicates, where Read1 and Read2 position were identical, were removed.
Data were filtered to exclude long terminal repeats, retrotransposons, telomeres, and the rDNA
Genome_build: Cer3H4L2 (https://github.com/Neale-Lab)
Supplementary_files_format_and_content: FullMap files containing sparsely-formatted, 1bp histograms detailing the total number of Watson (+) and  Crick (-) hits for all mapped base-pairs. 4-column format (Chr, Pos, Watson, Crick).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: cell culture

growth_protocol: Cells were grown overnight to saturation in 4 ml YPD medium (1% yeast extract, 2% peptone, 2% glucose supplemented with 0.5 mM adenine and 0.4 mM uracil) at 30 ˚C.

extract_protocol:
1x109 yeast cells were treated as described above, then spheroplasted in 1.5 ml spheroplasting buffer (1 M sorbitol, 50 mM NaHPO4 buffer pH 7.2, 10 mM EDTA) containing 200 μg/ml Zymolyase 100T (AMS Biotech) and 1% β-mercaptoethanol (Sigma) for 20 min at 37 ˚C. 2 µL Protease Inhibitor Cocktail and 2 µL Pefabloc (Sigma) were added before splitting into five aliquots of 400 µL.  1 ml ice-cold ethanol was added to 400 µL cell suspensions in microcentrifuge tubes in order to rapidly denature proteins in situ, mixed, incubated for 10 min on ice, and pelleted by centrifugation. The supernatant was thoroughly removed by aspiration, prior to addition of 200 µL 1x STE buffer (2% SDS, 0.5 M Tris pH 8.1, 10 mM EDTA, 0.05% bromophenol blue), cell disruption using a pestle (VWR), addition of a further 400 µL 1x STE buffer, and incubation for 10 min at 65 ˚C. Samples were cooled on ice and 500 µL Phenol-Chloroform-isoamyl alcohol (25:24:1; Sigma) was added. The mixtures were emulsified by shaking and pipetting 5 times with a 1 ml micropipette, prior to phase separation by centrifugation at 20,000 g for 20 min. By minimising mechanical shearing of the lysate prior to phenol chloroform extraction, peptides that are covalently linked to high molecular weight DNA segregate into the aqueous phase alongside other purified nucleic acids. Free protein, coated in SDS, will partition to the interphase. 500 µL of the aqueous phase was removed to a clean microcentrifuge tube, taking care not to disturb the interphase, and nucleic acids were precipitated with 1 ml ice-cold ethanol, pelleted by centrifugation, washed with ice-cold 70% ethanol, and dissolved in TE buffer overnight at 4 ˚C. Samples were then incubated with 0.2 mg/ml RNase A (Sigma) for 1 h at 37 ˚C; nucleic acids were precipitated with 1 ml ethanol, pelleted by centrifugation, washed twice with 70% ethanol and dissolved in TE overnight. Aliquots of nonproteolysed DNA  were combined to a total of 1 ml and sonicated to an average fragment size of 300-400 bp with Covaris (duty cycle: 10%, intensity/peak power incidence: 75W, cycles/burst: 200, time: 15 min). 1 ml of sonicated sample was diluted to reduce viscosity by addition of 1 ml TE. Triton-X100, N-Lauroylsarcosine sodium salt and NaCl were then added to complete the binding buffer (final concentrations: 0.3 M NaCl, 0.2% Triton-X100, 0.1% N-Lauroylsarcosine sodium salt). Each sample was divided over several Miniprep (QIAGEN) silica-fibre membrane spin columns, such that the total DNA loaded to each was approximately 20 µg. Under these high salt conditions, protein, but not nucleic acids, bind to the silica membrane, leading to selective retention of any covalent complexes (CCs). The flowthrough was reapplied to the column to improve yield. Columns were washed 6 times with 600 µL of TEN (10 mM Tris, 1 mM EDTA, 0.3 M NaCl) per 1 min wash to remove any residual non-CC DNA fragments, prior to elution with 100 µL TES (10 mM Tris, 1 mM EDTA, 0.5% SDS). The SDS detergent in the elution buffer releases interactions between protein and silica, thereby releasing bound CCs.
Eluted products were pooled to 500 µL in TES and incubated with 1 mg/ml Proteinase K (Sigma) for 30 min at 60 ˚C, prior to overnight ethanol precipitation at -80 ˚C with 1.41 ml ethanol, 0.2 mg/ml glycogen and 200 mM NaOAc. The DNA-glycogen precipitate was pelleted by centrifugation at 20,000 g for 1 hr at 4 ˚C, washed once with 1.5 ml 70% ethanol, and re-pelleted by centrifugation. The supernatant was aspirated and the pellet was air-dried for 10 min at RT, prior to solubilisation in 52 µL 10 mM Tris-HCl. DNA concentration was measured in a 2 µL sample with the Qubit (ThermoFisher) and High Sensitivity reagents.  The remaining 50 µL was used as input for one round of end repair and adapter ligation with NEBNext Ultra II DNA Library Preparation kit (NEB), according to manufacturer’s instructions, except for the use of a custom P7 adapter (see table).  The use of custom adapters is to allow differentiation of the sheared end (P7 adapter) from the Top2/Spo11 end (P5 adapter). After ligation of the P7 adapter, DNA was isolated with AMPure XP beads (Beckman Coulter) according to manufacturer’s instructions (beads:input of 78:90) and eluted in 50 µL 10 mM Tris-HCl. Samples were diluted 2-fold with 50 µL Tdp2 reaction buffer (100 mM TrisOAc, 100 mM NaOAc, 2 mM MgOAc, 2 mM DTT, 200 µg/ml BSA) and incubated with 3 µL of 10 µM recombinant human TDP2, for 1 h at 37 ˚C. DNA was isolated again with AMPure XP beads (beads:input of 103:103) and eluted in 52 µL 10 mM Tris-HCl. Next, a second round of adapter ligation was conducted using adapter P5 (see table), without prior end repair in order to prevent dephosphorylation of DNA 3’-phosphate termini which may be generated by TDP2 activity on 3’-CCs. After ligation of the P5 adapter to the Top2/Spo11-cleaved end, DNA was isolated with AMPure XP beads (beads:input of 78:90) and eluted in 17 µL 10 mM Tris-HCl. DNA concentration was measured in 2 µL using the Qubit. The remaining 15 µL was used as template for the PCR step of the NEBNext Ultra II PCR step using universal primer (P5 end) and indexed primers for multiplexing (P7 end), according to manufacturer's instructions. PCR reactions were diluted with 50 µL 10 mM Tris-HCl, DNA was isolated with AMPure XP beads (beads:input of 84:100) and eluted in 30 µL 1 mM Tris-HCl pH 8.1. Samples were then subjected to 200-600 bp size selection using the BluePippin (Sage Science), prior to quantification of molarity using the Bioanalyzer (Agilent).

treatment_protocol: Cells were diluted to OD600 0.5 in 100 ml YPD and grown until OD600 2. 50 ml cultures were then incubated for a further 4 h at 30 ˚C in the presence of either 1 mM VP16 or 2% DMSO.

tag: strain

tag: cell phase

value: vegetative (YPD)

tag: treatment


title: the fifth largest follicle (F5) rep1

description:
domestic goose
1HPGF5


title: CC-seq of S. cerevisiae Top2: pdr1, vegetative (YPD), UT, BioRep1, TechRep1

description: CC-seq map of Top2-DNA CCs

value: UT


title: CC-seq of S. cerevisiae Top2: pdr1sae2, vegetative (YPD), UT, BioRep1, TechRep1

description: CC-seq map of Top2-DNA CCs


title: CC-seq of S. cerevisiae Top2: pdr1mre11, vegetative (YPD), VP16, BioRep1, TechRep1

description: CC-seq map of Top2-DNA CCs


title: CC-seq of S. cerevisiae Top2: pdr1mre11, vegetative (YPD), VP16, BioRep2, TechRep1

description: CC-seq map of Top2-DNA CCs


title: CC-seq of S. cerevisiae Top2: pdr1mre11, vegetative (YPD), UT, BioRep2, TechRep1

description: CC-seq map of Top2-DNA CCs


title: CC-seq of S. cerevisiae Top2: pdr1sae2, vegetative (YPD), VP16, BioRep1, TechRep1

description: CC-seq map of Top2-DNA CCs


title: CC-seq of S. cerevisiae Top2: pdr1mre11, vegetative (YPD), UT, BioRep1, TechRep1

description: CC-seq map of Top2-DNA CCs


title: CC-seq of S. cerevisiae Top2: pdr1sae2, vegetative (YPD), VP16, BioRep2, TechRep1

description: CC-seq map of Top2-DNA CCs


title: PfSG-2


title: PyOO-2


title: CC-seq of S. cerevisiae Top2: pdr1, vegetative (YPD), UT, BioRep2 TechRep1

description: CC-seq map of Top2-DNA CCs


title: Samll white follicle rep4

description:
domestic goose
4HPG2-4


title: CC-seq of S. cerevisiae Top2: pdr1, vegetative (YPD), VP16, BioRep2, TechRep1

description: CC-seq map of Top2-DNA CCs


title: Input_left_MHb

status: Public on Sep 11 2019

city: New York

first: Laura

last: Kus

state: NY

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

description:
Pooled left MHb from 9 males, baseline
821_Chat_Input_left_MHb_GCCAAT_L007

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UCSC mm10 whole genome using STAR version 2.3.0e_r291, with default settings.
Quantification of aligned reads was done using htseq-count module, part of the ‘HTSeq’ framework, version 0.6.0, using default settings, with ‘union’ mode to handle reads overlapping more than one feature.
Differentially expressed genes were identified by performing a negative binomial test using DESeq2 (R-package version 1.4.5) with default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Counts text

organism: Mus musculus

source_name: Medial Habenula

growth_protocol: All mice were maintained on a 12h light-dark cycle with ad lib access to food and water. Adult mice were used for all experiments (>8 weeks of age).

extract_protocol:
Brain regions of interest were microdissected, and homogenized immediately for IP using magnetic beads conjugated to anti-GFP. Total RNA was extracted from both the total homogenate (INPUT) and the IP fraction.
Ovation RNA-Seq System V2 kit (Nugen, Cat# 7102) was used with 10ug of RNA for MHb samples or 500pg of RNA for IPN samples for generation of SPIA cDNA. 1ug of SPIA cDNA was fragmented to 250bp before proceeding with library prepartion using the TruSeq DNA Nano LT Sample Prep Kit (Illumina, Cat# 20015964).

treatment_protocol: Animals were sacrificed by live decapitation, brains were rapidly removed and regions of interest dissected on ice. See sample details for specific drug treatments.

tag: background strain

tag: transgene(s)

value: ChAT-TRAP (DW167)

tag: fraction

value: Input


title: Saccharin_saline_input2

description:
Pooled 4 animals, 6wk 0.2% saccharin in drinking water, ip saline 3hr before tissue collection
741_Chat_Saccharin_saline_input2_GCCAAT_L002


title: Input_right_MHb

description:
Pooled right MHb from 9 males, baseline
823_Chat_Input_right_MHb_ACAGTG_L003


title: T-ALL4 (RNA-seq)

status: Public on Aug 04 2019

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

country: Germany

institute: Helmholtz Centre for Infection Research

data_processing:
Read alignment: STAR aligner version 2.5.0c was used to map reads against the reference genome hg19. Only uniquely mapping reads were kept (specific parameters: --trim5p=13, --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.05)
Deduplication: Duplicated reads were excluded using picard-tools version 2.6.0.
Read counting: Reads were counted on a stranded gene-basis within annotated exons downloaded from Ensembl Genes V75 using the ngsutils tool bamutils count (special paramters: -uniq, -multiple complete, -library RF).
Normalization: edgeR version 3.14.0 was used to normalize read counts per sample and genes were filtered for counts-per-million > 1. CDS length from Ensembl Genes V75 was used to calculate FPKM values for filtered genes.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM table

organism: Homo sapiens

source_name: Peripheral blood primary T-ALL cells

growth_protocol: Primary T-ALL cells isolated from the peripheral blood of T-ALL patients were xenogroafted in immunocompromised NOD SCID gamma mice (NSG) . Following xenograft and when the tumor bueden in pheripheral blood reached 80% the mice were the spleen was harvested and splenocytes were used for the RNA-Seq analysis.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit using Qiagen kit (Catalog no: 74106) folllowing manufacturer's guidelines.
The libraries were prepared using NEXTflex Rapid Directional RNA-Seq Kit from Bioo Scientific (Catalog no: 5138-07) folllowing manufacturer's guidelines.

value: Peripheral blood

tag: cell type

value: primary T-ALL cells

tag: disease state

value: T cell acute lymphoblastic leukemia


title: T-ALL1 (RNA-seq)


title: T-ALL3 (RNA-seq)


title: T-ALL1 input (ChIP-seq)

data_processing:
Read alignment: Reads were aligned against the reference sequence hg19 with bowtie2 (version 2.3.1) with standard parameters and only uniquely mapped reads were kept with MAPQ > 20.
Deduplication: Aligned reads were filtered for duplicated reads using picard-tools version 2.6.0.
Peak-calling: Peak calling for CTCF and H3K27ac was performed using MACS2 (version 2.0.1) using narrow (CTCF) and broad (--broad; H3K27ac) option (sepcial parameters: --no-model).
Differential binding: To identify differentially bound peaks, we performed diffBind (version 2.2.12) analysis, using the normalization option DBA_EDGER.
Bigwig: For visualization purposes, we generated fold-enrichment bigwig files by applying MACS2 (version 2.0.1) bdgcmp over input (-m FE)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, peak (bed)

growth_protocol: CUTLL1 cells were grown in RPMI medium with 10% FBS ; Primary T-ALL cells isolated from the peripheral blood of T-ALL patients were xenogroafted in immunocompromised NOD SCID gamma mice (NSG) . Following xenograft, and when the tumor bueden in pheripheral blood reached 80%, the mice were sacrificed and the spleen was harvested and splenocytes were used for the Chip-Seq analysis;  Healthy T cells were purchased from Lonza (catlog no: 2W-200)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
libraries were prepared using Kapa Hyper prep kit (Catalog no: KK8500) following manufacturer's guidelines

treatment_protocol: CUTLL1 cells were treated with gamma-secretase inhibitor (1 uM) for 72 hours or BET inhibitor (JQ1, 500 nM) for 24h or CDK7 inhibitor (THZ1, 100 mM) for 24 hours.

value: Primary T-ALL

tag: chip antibody


title: Large white follicle rep4

description:
domestic goose
4HPG4-6


title: T-ALL3 (Hi-C)

description:
Primary T-ALL, classified as canonical T-ALL based on transcriptomic profiling. Enzymatic restriction was peformed using commercial Arima kit.
HiC_cscore_compartment-scores.tsv
HiC_hicratio-scores.tsv

data_processing:
Read alignment: bowtie2 2.2.3. Paired-end reads were mapped against the hg19 reference sequence using bowtie2 (special paramters: --very-sensitive-local --local)
Filtering: GenomicTools "gtools-hic filter". Discards read-pairs marked as multihits, only one mappable read, positional duplicates, low mapping quality (MAPQ < 20), self-ligated fragments, short-range interactions (<25 kb)
Matrix generation: HicBench. For each sample and each chromosome, a matrix with binned interactions (bin-size 40kb) was generated.
Normalization: ICE normalization as described in Imakaev et al. (2012) was employed first. We then applied normalization by distance as recently described (Gong et al., 2018)
Topologically Associated Domains (TAD) calls: TADs were called using the algorithm developed within hic-bench, setting the insulating window to 500kb.
Genome_build: hg19
Supplementary_files_format_and_content: TAD bed files, scores.tsv files

growth_protocol: CUTLL1 and Jurkat cells were grown in RPMI medium with 10% FBS ; Primary T-ALL cells isolated from the peripheral blood of T-ALL patients were xenogroafted in immunocompromised NOD SCID gamma mice (NSG) . Following xenograft, T-ALL cells were isolated from spleen by flow cytometer using hCD45 as marker;  Healthy T cells were purchased from Lonza (catalog no: 2W-200)

extract_protocol:
Nuclear extraction and DNA purification using Amicon Ultra 30K
End-repair was performed using T4 DNA polymerase (NEB), T4 DNA polynucleotide kinase (NEB), Klenow (NEB) and dNTPs in 1× T4 DNA ligase reaction buffer (NEB), followed by dATP-addition with Klenow. Paired-end (PE) adapters (Illumina) were ligated to DNA fragments using 15 U of the T4 DNA ligase (Invitrogen) for 2 hours at room temperature. Bead-bound DNA was amplified with 6 PCR amplification cycles using PE PCR 1.0 and PE PCR 2.0 primers (Illumina). Library prepartion of samples prcoessed using Arima HiC kit were prepared using Kap Hper library prep kit (KK8504)as per manufacturer's guidelines.

treatment_protocol: CUTLL1 cells were treated with DMSO or gamma-secretase inhibitor (1 uM) for 72 hours or THZ1 (100 nM) for 24 hours.

tag: enzymatic restriction

value: commercial Arima kit


title: T-ALL2 (Hi-C)


title: T-ALL1 CTCF rep2 (ChIP-seq)

description:
TALL1_CTCF_narrow-peaks.bed
TALL1_CTCF_FE.bw

value: CTCF (D31H2; Catalog no:3418)


title: T-ALL1 CTCF rep1 (ChIP-seq)


title: 201704-olig2 (ChIP-seq)

status: Public on Oct 31 2019

city: Shanghai

first: Guofeng

last: Meng

address: Jinke 3528

institute: Shanghai University of Traditional Chinese Medicine

data_processing:
The adaptors were cut using Ngmerge
Pair-end reads were aligned to hg38 genome using bowtie2 under default parameter setting
The TF binding sites were detected by macs2
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak

source_name: brain prefrontal cortex region tissues

extract_protocol:
Chromatin was sonicated by Bioruptor (Diagenode, Belgium) under the condition as follows: 20 cycles of 30 s on, 60 s off. The sonicated chromatin was spun down at 12,000 rpm for 10 min at 4 °C to collect the chromatin. Add antibody (10 μg) to the soluble chromatin (80 μg), and incubate at 4 °C with rotation overnight. Protein A/G Dynabeads (10 μl of beads per 1 μg of antibody, Life Tech, 10004D) were washed three times with Low Salt Wash Buffer. The washed Dynabeads were added to the soluble chromatin and antibodies, incubated at 4°C for 4 h with rotation. The magnetic Dynabeads were pelleted by placing the tubes in a magnetic rack and were sequentially washed once with Low Salt Wash Buffer, once with High-salt Wash Buffer, once with LiCl Wash Buffer. Wash the beads three times with TE buffer. Remove any supernatant remaining after the last washing. The beads were resuspended in 150 μl of Elution Buffer (50 mM Tris•Cl pH 8.0, 10 mM EDTA, 1% SDS), followed by incubation for 15 min at 65 °C. Repeat step 7 again, combine the elution, then you have 300 μl of the eluted DNA solution. Add 1 μl of high concentration RNase A (10 mg/ml) to the eluted DNA solution and the Input samples (500 μl), respectively. Incubate them at 37 ℃ for 1 h. Reverse formaldehyde crosslinks by respectively adding 12.5 μl or 55 μl of 5 M NaCl to the eluted DNA solution and the Input samples to a final concentration of 0.2 M. Incubate samples at 65 ℃ (650 rpm) for more than 8 h (less than 16 h).  Add both 80.5 μl of ddH2O and 5 μl of 20 mg/ml Proteinase K to the eluted DNA solution, and just 5 μl of Proteinase K to the Inputs. Incubate at 56 ℃ for 2 h. Extract once with 400 μl of phenol/chloroform/isoamyl alcohol, and once with 400 μl of chloroform/isoamyl alcohol (optional). Transfer 355 μl of supernatant to a new tube. Add 55 μl or 40 μl of 3 M NaAc (pH 5.2, 0.3 M final) to the Input samples and eluted DNA solution, 5 μl of glycogen each sample and mix well. Add 800 μl (two-fold volume) of absolute ethanol. Precipitate at -20 ℃ overnight or at -80 ℃ for 4 h. Centrifuge at 14000 rmp for 20 min at 4 ℃. Wash once with 75% ethanol and store at -20 ℃.
The library is constructed under the protocol of Iillumina

value: normal

tag: Sex

value: male

tag: braak

value: Olig2 (RnD, catalog# AF2418, lot# UPA0718031)

value: brain prefrontal cortex region tissues


title: T-ALL1 (Hi-C)


title: Patient12muscle_Diff. SMC

status: Public on Jul 13 2019

type: RNA

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

hyb_protocol: Hybridization was performed according to CustomArray ElectraSense™ Hybridization and Detection protocol. Hybridization mix contained 2.5 ug of labeleled DNA library, 6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt solution, 100 ng/ul sonicated calf thymus gDNA, 0,05% SDS. Hybridization mix was incubated with chip overnight at 50ºC.

scan_protocol: Hybridization efficiency was detected electrochemically using CustomArray ElectraSense™ Detection Kit and ElectraSense™ 4X2K/12K Reader.

data_processing: The data were normalised using quantile normalisation in R.

label: biotin

source_name: multipotent mesenchymal stromal cells (MMSC) isolated from skeletal muscle, differentiated to myotube-like structures

label_protocol: Complete Whole Transcriptome Amplification WTA2 Kit  (Sigma) was used for reverse transcription and library amplification. Manufacturer's protocol was modified by adding to amplification reaction dNTP mix containing biotinylated dUTP, resulting to final proportion dTTP/biotin-dUTP as 5/1.

growth_protocol: Samples were obtained from six human donors of gingiva and skin tissues (3 women and 3 men, mean age 33±4 years) and six donors of muscle tissues (3 women and 3 men, mean age 63 ± 3 years). Biopsies of the alveolar mucosa were taken from the retromolar area and attached gingiva from the distal mandibular molar level. Samples of the skin from the region behind the ear (N=3) were taken from the same donors. The biopsy specimens of the quadriceps femoris muscle were taken during standard surgical treatment of the atherosclerotic vascular lesions of lower limbs. Biopsy samples were placed in sterile medium containing α-MEM (Sigma), 2% FBS (HyClone), penicillin (200 U/mL), streptomycin (200 mg/mL), and amphotericin (200 U/mL) (Stem Cell Technologies), labeled and delivered at +4°С to laboratory within 2 hours.  All biopsy samples were processed using similar protocol as follows. Multipotent mesenchymal stromal cells (MMSC) were isolated from alveolar mucosa (AMC), attached gingiva (AGC) and skeletal muscle (SMC) biopsy samples, and skin fibroblasts from the skin. Biopsy sample was washed with α-MEM (Sigma) supplemented with gentamicin (50 µg/mL) (Sigma). A sample was transferred into 15 mL tube in α-MEM supplemented with 10% FBS (HyClone), gentamicin (20 µg/mL), 0.05% solution of collagenase type II (Sigma) and incubated for 12 hours at 37ºС. Before enzymatic digestion skeletal muscle samples were minced. After that cell suspension was centrifuged at 200 g for 10 min. The cell pellet was resuspended in culture medium DMEM/F12 (HyClone) supplemented with 20% FBS (HyClone), gentamicin (20 µg/mL) and plated in culture flasks (NUNC) at density of 3–5×104 cells/cm2. Cells were cultured at 37°С, humidity 95% and 5% СО2 with medium change every 3 days. Cell cultures were passaged at 50% confluence. Visual observation of culture growth and cell morphology was conducted by phase contrast microscopy. Cell cultures at passage 2 were used for research experiments.

extract_protocol: Cells were harvested with 0.25% Trypsin –EDTA solution (STEMCELL Technologies Inc). Cell’s suspensions were stabilized in RNAlater (Qiagen, Germany), aliquoted by 0.3 million cells per tube and stored at −80°C. Before the extraction RNAlater was removed and cells were resuspended  in TRIzol Reagent (Life Technologies, USA). RNA extraction was performed using Direct-zol™ RNA MiniPrep (Zymo Research) kit. RNA was quantified with Nanodrop (Thermo Fisher Scientific).

treatment_protocol: To induce myogenic differentiation, AMC and SMC were seeded at passage 2 at density of 5×105 cells/cm2 and cultured in DMEM/F12 supplemented with 20% FBS (HyClone) until 90-100% confluent monolayer was formed. Then culture medium was replaced with low glucose DMEM (HyClone) supplemented with 2% horse serum (BioInd) and cells were incubated for 5-10 days at 37°С, humidity 95% and 5% СО2 until myotube-like structures formed.

tag: patient

value: Patient 12

tag: biopsy

value: skeletal muscle

tag: myogenic differentiation

value: yes


title: Patient12muscle_SMC

source_name: multipotent mesenchymal stromal cells (MMSC) isolated from skeletal muscle

value: no


title: Patient11muscle_Diff. SMC

value: Patient 11


title: T-ALL2 (RNA-seq)

tag: tissue


title: T-ALL4 (Hi-C)


title: Patient3_Diff. AMC

source_name: multipotent mesenchymal stromal cells (MMSC) isolated from alveolar mucosa, differentiated to myotube-like structures

value: Patient 3

value: alveolar mucosa


title: Patient3_AMC

source_name: multipotent mesenchymal stromal cells (MMSC) isolated from alveolar mucosa


title: Patient5_AMC

value: Patient 5


title: Patient5_Diff. AMC


title: Patient5_Skin

source_name: skin fibroblasts

value: skin


title: Patient2_Diff. AMC

value: Patient 2


title: Patient5_AGC

source_name: multipotent mesenchymal stromal cells (MMSC) isolated from attached gingiva

value: attached gingiva


title: Patient4_Skin

value: Patient 4


title: Patient4_Diff. AMC


title: Patient4_AGC


title: Patient2_Skin


title: Patient3_Skin


title: Patient2_AGC


title: Patient1_Diff. AMC

value: Patient 1


title: Patient3_AGC


title: Patient1_AMC


title: Patient4_AMC


title: Patient1_AGC


title: Patient1_Skin


title: Patient6_AGC

value: Patient 6


title: Patient6_Skin


title: Patient6_AMC


title: Patient10muscle_Diff. SMC

value: Patient 10


title: TBP-ERT2-3HA ChIP-seq 4OHT 360 min

status: Public on Jul 03 2019

city: Boston

first: Yuko

last: Hasegawa

state: MA

address: 240 Longwood Ave

department: BCMP

institute: Harvard Medical School

data_processing:
ChIP-seq reads were aligned to the custom genome containing hg38 and sacCer3 assembly using bowtie2 using parameter --sensitive.
PCR duplicates were removed using picard MarkDuplicates and mapped reads with low quality score (less than 30) were excluded using samtools.
Peaks calling was performed with MACS2 using input from each expetiment as a reference with the following setting: -q 0.01.
bedGraph files were created by MACS2 pileup.
Values in bedGraph were normalized to reference-adjusted reads per million (RRPM) calculated as deviding human ChIP-seq score by total yeast mapped reads.
bedGraph files were converted to bigWig by UCSC bedGraphToBigWig program.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig, Scores represent Reference-adjusted RPM

growth_protocol: pCMV-TBP-ERT2-3HA construct was transfected to HEK293 (ATCC) cells, and the stable line was established by G418 selection. Cells were routinely cultured in phenol-red free DMEM containing 10% FBS.

extract_protocol:
Cell Lysates were clarified from sonicated nuclei and ERT2-3HA fused TBP-DNA complexes were isolated with HA antibody.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645).

treatment_protocol: Cells were treated with EtOH or 100nM 4OHT.


title: TBP-ERT2-3HA ChIP-seq 4OHT 1440 min


title: Patient10muscle_SMC


title: Patient6_Diff. AMC


title: Patient11muscle_SMC


title: TBP-ERT2-3HA ChIP-seq 4OHT 30 min


title: TBP-ERT2-3HA ChIP-seq 4OHT 60 min


title: Patient9muscle_SMC

value: Patient 9


title: Patient9muscle_Diff. SMC


title: TBP-ERT2-3HA ChIP-seq 4OHT 15 min


title: Patient8muscle_SMC

value: Patient 8


title: Patient7muscle_Diff. SMC

value: Patient 7


title: TBP-ERT2-3HA ChIP-seq 4OHT 10 min


title: input DNA 10 min


title: Patient8muscle_Diff. SMC

value: skeletal muscle


title: input DNA 0 min


title: AN03398_cyto

status: Public on Jun 25 2019

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description: processed data file: COUNTS_Cyto.txt

data_processing:
Single-end reads were aligned with STAR 2.5.2b using options "“--outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic" to a reference sequence (GRCh37 from Ensemble)
RNA-seq Counts values were quantified using HTSeq python suite based on Homo_sapiens.GRCh37.87.gtf from Ensemble based on protein coding genes and exons.
Genome_build: Human hg19 (GRCh37)
Supplementary_files_format_and_content: Input tables and demographics are included as tab separated files.

source_name: Frozen Brain Tissue

extract_protocol:
nuclear extraction: Tissue isolated from Brodmann Area 46 from 40 individuals with schizophrenia and 49 matched controls.700 mg of frozen postmortem brain was homogenized with lysis buffer using a dounce homogenizer. Brain lysate was placed on a sucrose solution to create a concentration gradient. Ultracentrifuge was used to separte nuclei and cytoplasmic fraction.
FANS protocol: Nuclei were resuspended in PBS plus RNAse inhibitors and incubated with mouse alexa488 conjugated anti-NeuN (1:200) (#MAB377X, Millipore, Billerica, MA) and rabbit alexa555 conjugated anti-OLIG2 (1:75) (#AB9610-AF555, Millipore) antibodies with 0.5% BSA. Immuno-labeled nuclei were collected as NeuN-positive or OLIG2-positive populations by fluorescence-activated cell sorting (FACS).
RNA extraction: Total RNA were purified from each nuclei population using a ZR-Duet DNA/RNA MiniPrep (Plus) kit according to the manufacturer's instruction. 200 ng total RNA from each sample was treated for ribosomal RNA (rRNA) removal using the Low Input RiboMinus Eukaryote System v2 (#A15027, ThermoFisher) according to the manufacturer's instruction.
Total RNAs with an average RIN value of 7.5±0.16 were used for RNA-seq library preparation. 50 ng of total RNA after rRNA removal was subjected to fragmentation, first and second strand syntheses, and clean up by EpiNext beads (#P1063, EpiGentek, Farmingdale, NY). Second strand cDNA was adenylated, ligated and cleaned up twice by EpiNext beads. cDNA libraries were amplified by PCR, and cleaned up twice by EpiNext beads. cDNA library quality was quantified by a 2100 Bioanalyzer using an Agilent High Sensitivity DNA Kit (#5067-4626, Agilent, Santa Clara, CA). Barcoded libraries were pooled and underwent 75 bp single-end sequencing on an Illumina NextSeq 500.

tag: subject id

value: Cyto

tag: diagnosis

value: Control

value: F

tag: age

tag: pmi

tag: hemisphere

value: L

tag: brodman area

value: Brodmann Area 46

tag: brainbank

value: HBTC

tag: rin


title: TBP-ERT2-3HA ChIP-seq 4OHT 5 min


title: Patient2_AMC

value: alveolar mucosa

value: no


title: input DNA 5 min


title: TBP-ERT2-3HA ChIP-seq 4OHT 90 min


title: input DNA 90 min


title: AN09634_cyto

description: processed data file: COUNTS_Cyto.txt

tag: cell type

value: Schizophrenia

value: M

value: R


title: AN18099_cyto

description: processed data file: COUNTS_Cyto.txt


title: 1538_cyto

description: processed data file: COUNTS_Cyto.txt

value: Ctlab


title: 3611_cyto

description: processed data file: COUNTS_Cyto.txt

value: HSB


title: 3602_cyto

description: processed data file: COUNTS_Cyto.txt


title: Miami0001_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt

source_name: frozen brain tissue_Control_Olig2

value: Miami


title: Patient7muscle_SMC


title: 4730_cyto

description: processed data file: COUNTS_Cyto.txt


title: AN16799_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: AN10090_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: AN05483_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: AN15240_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 3545_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 3602_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: AN03398_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 1541_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 3590_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 4615_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 3586_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 1539_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 1532_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 1528_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 1536_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 1526_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 1527_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 1524_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 1530_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 1525_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 1529_Control_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: AN18099_Schizo_Olig2

description: processed data file: COUNTS_OLIG2.txt

source_name: frozen brain tissue_Schizo_Olig2


title: AN17799_Schizo_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 4804_Schizo_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 4395_Schizo_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: CC-seq of S. cerevisiae Top2: pdr1sae2, vegetative (YPD), UT, BioRep2, TechRep1

description: CC-seq map of Top2-DNA CCs

tag: strain

tag: cell phase

value: vegetative (YPD)

tag: treatment

value: UT


title: 1514_Schizo_Olig2

description: processed data file: COUNTS_OLIG2.txt

tag: Sex


title: 1518_Schizo_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 1515_Schizo_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 1520_Schizo_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 1523_Schizo_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 4361_Schizo_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 1513_Schizo_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 4336_Schizo_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 1511_Schizo_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 1507_Schizo_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 1508_Schizo_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: Miami0002_Control_NeuN

description: processed data file: COUNTS_NeuN.txt

source_name: frozen brain tissue_Control_NeuN

value: NeuN


title: 1505_Schizo_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: Miami0001_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: AN15240_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: AN05483_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: AN15472_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: AN10090_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 3602_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: AN03398_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 3611_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 4615_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 3545_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 3590_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 3586_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1540_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1506_Schizo_Olig2

description: processed data file: COUNTS_OLIG2.txt


title: 1539_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: AN16799_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1538_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1525_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1536_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1528_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: AN17799_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt

source_name: frozen brain tissue_Schizo_NeuN


title: 1526_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1532_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: AN18099_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1529_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 4448_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 4504_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 4395_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1527_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 4361_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: AN09634_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1530_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 4804_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 4730_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 4336_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1541_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1520_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1515_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1514_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1511_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1510_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1512_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1513_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1518_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1524_Control_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1508_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1523_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1507_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 1506_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt


title: 4730G

city: Atlanta

first: Soojin

middle: V

last: Yi

state: GA

address: 950 Atlantic Dr

department: School of Biology

institute: Georgia Institute of Technology

description:
54samples_ALLchr_biallelic_MAF005_HWE001_GENO005_PASS.fam
54samples_ALLchr_biallelic_MAF005_HWE001_GENO005_PASS.bed
54samples_ALLchr_biallelic_MAF005_HWE001_GENO005_PASS.bim

data_processing:
Library strategy: Whole-genome sequencing
Quality and adapter trimming of raw reads was performed using TrimGalore (Babraham Institute). Reads were mapped to the human GRCh37 reference genome using BWA (version 0.7.4) and duplicates were removed using picard (version 2.8.3).
We identified genetic polymorphism from re-sequencing data following GATK v3.7 best practices workflow (McKenna, et al. 2010). We used HapMap 3.3, Omni 2.5M, 1000 Genomes Phase I and dbSNP 138 as training datasets for variant recalibration. We filtered variant calls with high genotype quality (GQ >=20.0).
We kept variants with genotype missingness below 5%, Hardy-Weinberg equilibrium test P>0.001 and minor allele frequency above 5%. The total genotyping rate was >0.99 and the maximum per individual missingness was 0.1%.
Genome_build: GRCh37
Supplementary_files_format_and_content: plink files

source_name: Brain BA46

extract_protocol:
Genomic DNA was isolated from 1mg to 5mg of tissue sample, using the Qiagen DNeasy Blood and Tissue DNA extraction kit according to manufacturer’s instructions. The extracted DNA was suspended in TE buffer and quantified by Qubit (Thermo Fisher Scientific).
Libraries were made with In-House Illumina sequencer compatible protocol. The extracted DNA was fragmented by S-series focused ultrasonicator (Covaris) using the “200bp-target peak size protocol”. Fragmented DNA was then size selected (200bp-600bp) with Agencourt aMPure XP bead-based (Beckman Coulter Cat. No. A63880) size selection protocol (Mark. A. Urich et al. 2015). The DNA End repair step was performed with End-It DNA end repair kit (Epicentre, Cat. No. ER81050. After End repair step, A-tailing (NEB, cat. No. M0202) and Ligation steps are performed to ligate methylated adaptors.

treatment_protocol: Human post-mortem brain tissue from the Brodmann Area 46 (BA46) was obtained.

value: Brain

tag: brain region

value: Brodmann Area 46 (BA46)

tag: disease state

value: Schizo

value: female


title: AN18099G

value: male


title: AN09634G


title: 1505_Schizo_NeuN

description: processed data file: COUNTS_NeuN.txt

value: F

value: L

value: Brodmann Area 46


title: AN05483G

value: Control


title: 4395G


title: 4448G


title: 4804G


title: AN17799G


title: AN16799G


title: 4504G


title: 3590G


title: Miami0001G


title: AN03398G


title: AN15240G


title: 3611G


title: AN10090G


title: 1541G


title: 1538G


title: 1539G


title: 1536G


title: 1527G


title: 1525G


title: 1520G


title: 1518G


title: 1515G


title: 1514G


title: 4615G


title: 1511G


title: 1507G


title: 4361G


title: 1510G


title: 4336G


title: 3602G


title: 1524G


title: 1512G


title: 3586G


title: 3545G


title: 1506G


title: 1523G


title: 1531G


title: 1522G


title: 1534G


title: 1508_WGBS_Olig2

data_processing:
Quality and adapter trimming was performed using TrimGalore version 0.4.1 (Babraham Institute).
Reads were mapped to the human GRCh37 reference genome using Bismark version: v0.14.4 (Krueger and Andrews 2011) and Bowtie
Methylation calling was performed after deduplication using Bismark
Bsseq bioconductor package and Bsmooth (Hansen et al 2012) were used to process CpG methylation data
Genome_build: GRCh37
Supplementary_files_format_and_content: Methylated read count and coverage for CpGs

extract_protocol:
Genomic DNA was isolated from 1mg to 5mg of tissue sample, using the Qiagen DNeasy Blood and Tissue DNA extraction kit according to manufacturer’s instructions. The extracted DNA was suspended in TE buffer and quantified by Qubit (Thermo Fisher Scientific).
Libraries were made with In-House Illumina sequencer compatible protocol. The extracted DNA was fragmented by S-series focused ultrasonicator (Covaris) using the “200bp-target peak size protocol”. Fragmented DNA was then size selected (200bp-600bp) with Agencourt aMPure XP bead-based (Beckman Coulter Cat. No. A63880) size selection protocol (Mark. A. Urich et al. 2015). The DNA End repair step was performed with End-It DNA end repair kit (Epicentre, Cat. No. ER81050. After End repair step, A-tailing (NEB, cat. No. M0202) and Ligation steps are performed to ligate methylated adaptors. Bisulfite treatment of genomic DNA was performed using the MethylCode Bisulfite Conversion Kit (Life technologies). Purified genomic DNA was treated with CT conversion reagent in a thermocycler for 10 minutes at 980C, followed by 2.5 hours at 640C. Bisulfite-treated DNA fragments remain Single-stranded as they are no longer complementary. Low-cycle (4-8) PCR amplification was performed with Kapa HiFi Uracil Hotstart polymerase enzyme (KAPA Biosystems, cat. No. KK2801) which can tolerate Uracil residues. The final library fragments contain Thymines and Cytosines in place of the original unmethylated cytosine and methylated cytosines, respectively.

treatment_protocol: Human post-mortem brain tissue from the Brodmann Area 46 (BA46) was obtained.  NeuN+ and OLIG2+ nuclei were purified  employing fluorescence activated nuclei sorting (FANS)

value: brain


title: 1510_WGBS_Olig2

value: M


title: 1521G


title: 1532G


title: AN09634_WGBS_Olig2


title: 1513G


title: 1518_WGBS_Olig2


title: AN18099_WGBS_Olig2


title: 1515_WGBS_Olig2


title: 1505G


title: 1508G


title: 1517G


title: 1537G


title: AN09634_WGBS_NeuN


title: AN18099_WGBS_NeuN


title: 1533G


title: 4804_WGBS_NeuN


title: AN16799_WGBS_Olig2


title: AN15240_WGBS_Olig2


title: 4730_WGBS_NeuN


title: 4730_WGBS_Olig2


title: AN03398_WGBS_Olig2


title: 1535G


title: 1509G


title: 4804_WGBS_Olig2


title: 3611_WGBS_Olig2


title: 1522_WGBS_NeuN


title: 1519_WGBS_NeuN


title: 1513_WGBS_Olig2


title: 1533_WGBS_NeuN


title: 1514_WGBS_Olig2


title: 4504_WGBS_Olig2


title: 1521_WGBS_NeuN


title: 3602_WGBS_Olig2


title: 1509_WGBS_NeuN


title: 4448_WGBS_Olig2


title: Miami0001_WGBS_Olig2


title: 1519G


title: 1516_WGBS_NeuN


title: AN17799_WGBS_NeuN


title: 1520_WGBS_Olig2


title: 1537_WGBS_NeuN


title: 3590_WGBS_Olig2


title: 3590_WGBS_NeuN


title: 1516G


title: 1535_WGBS_NeuN


title: 1525_WGBS_Olig2


title: 4395_WGBS_Olig2


title: 4395_WGBS_NeuN


title: 4504_WGBS_NeuN


title: 1538_WGBS_Olig2


title: AN17799_WGBS_Olig2


title: 1536_WGBS_Olig2


title: 4448_WGBS_NeuN


title: 1527_WGBS_Olig2


title: 1539_WGBS_Olig2


title: AN10090_WGBS_NeuN


title: AN05483_WGBS_Olig2


title: AN10090_WGBS_Olig2


title: Miami0001_WGBS_NeuN


title: 4615_WGBS_Olig2


title: 1532_WGBS_Olig2


title: AN05483_WGBS_NeuN


title: AN15240_WGBS_NeuN


title: 3611_WGBS_NeuN


title: AN16799_WGBS_NeuN


title: 1541_WGBS_NeuN


title: 3602_WGBS_NeuN


title: 1536_WGBS_NeuN


title: 1538_WGBS_NeuN


title: 1527_WGBS_NeuN


title: 1541_WGBS_Olig2


title: 1532_WGBS_NeuN


title: AN03398_WGBS_NeuN


title: 1511_WGBS_Olig2


title: 1518_WGBS_NeuN


title: 1514_WGBS_NeuN


title: 1515_WGBS_NeuN


title: 1513_WGBS_NeuN


title: 1511_WGBS_NeuN


title: 1510_WGBS_NeuN


title: 1507_WGBS_Olig2


title: 1508_WGBS_NeuN


title: 4361_WGBS_Olig2


title: 4615_WGBS_NeuN


title: 1507_WGBS_NeuN


title: 1539_WGBS_NeuN


title: 3586_WGBS_Olig2


title: 1524_WGBS_Olig2


title: 4361_WGBS_NeuN


title: 4336_WGBS_Olig2


title: 3545_WGBS_Olig2


title: 1505_WGBS_NeuN


title: 1505_WGBS_Olig2


title: 1524_WGBS_NeuN


title: 3545_WGBS_NeuN


title: 3586_WGBS_NeuN


title: 1523_WGBS_Olig2


title: 1512_WGBS_NeuN


title: 1523_WGBS_NeuN


title: 4336_WGBS_NeuN


title: 1517_WGBS_NeuN


title: 1534_WGBS_NeuN


title: 1531_WGBS_NeuN


title: Stages 3 to 6, Protocol x1, Stage 3 complete

status: Public on May 10 2019

city: Cambridge

first: Adrian

last: Veres

state: Massachusetts

address: 7 Divinity Ave

institute: Harvard University

data_processing:
All processing steps from raw fastq files to count matrices were performed using the custom pipeline for inDrops data analysis (www.github.com/indrops/indrops) using the the following parameters specified in the YAML file: [trimmomatic arguments]: LEADING: "28", SLIDINGWINDOW: "4:20", MINLEN: "30". [output_arguments]: filter_alignments_to_softmasked_regions: True. All other parameters were used as in the default_parameters file in the repository github.com/indrops/indrops, commit hash 8a9167.
Genome_build: GRCh38.88
Supplementary_files_format_and_content: '*.raw_indrops_counts.*' files are the raw, unfiltered output from the Indrops processing pipeline. The first column indicates the barcode label using the Indrops pipeline nomenclature, all folllowing columns are UMIFM counts as defined in Klein et al. (2015). The gene corresponding to each column is listed in the header line.
Supplementary_files_format_and_content: '*.processed_counts.*' are filtered counts files, removing undetected genes and filtering cells using the thresholds described in the methods section of Veres et al. 2019. The first column indicates the cell label, all following columns are UMIFM counts for the gene indicated in the header row.
Supplementary_files_format_and_content: '*.cell_metadata.*' files contain metadata associated for all filtered cells in the each dataset. The first row is a header detailing the type of data in each column. These include TSNE coordinates, cluster label annotations and pseudotime values (as appropriate).
Supplementary_files_format_and_content: code_analysis_files.tar is a tarball of all files (primarily loom-formatted) used in generating the analysis, with the accompanying code at https://github.com/meltonlab/scbeta_indrops

molecule: polyA RNA

source_name: in vitro differentiated pluripotent stem cell

growth_protocol: Human embryonic and pluripotent stem cells were maintained and differentiated as described in the methods of (Veres et al. 2018). Differentiation was carried out using step-wise protocols aimed at gradually producing beta cells in vitro.

extract_protocol:
Differentiated clusters were prepared for single cell RNA sequencing as follows: 1-2 mL suspension culture was sampled from the spinner flask, dissociated with TrypLE Express (5-15 minutes at 37 °C), quenched with cold PBS + 1% BSA and gently dispersed with a P1000 pipette. Cells were then centrifuged (300 rpm, 3 min), resuspended in cold PBS+1% BSA and filtered through a 70 µm mesh filter. Centrifugation, resuspension and filtering was repeated a total of 3 times. Cells were then counted and resuspended to the working dilution for inDrops (100,000 cells/mL) in 1X PBS with 13% Optiprep (Sigma; D1556).
Single cell RNA sequencing was carried out using the inDrops platform, as previously described (Klein 2015, Zilionis 2016). Most samples were run using ‘inDrops v2’ barcoded hydrogel beads (1 Cell Bio, Harvard Single Cell Core), and one experiment used ‘inDrops v3’ beads (Harvard Single Cell Core). Following the inDrops protocol, each biological sample was split into several aliquots of 1000-3000 cells after encapsulation. At least two library aliquots were prepared separately from each sample, indexing using recommended index sequences, pooled and sequencing on a NextSeq 500 (Illumina).

tag: experiment

value: Stages 3 to 6 timecourse

value: SC-beta protocol x1

tag: Stage

value: Stage 3


title: 1506_WGBS_NeuN

tag: tissue

tag: subject id


title: N720_S505_7: CD69neg scRNA-seq

status: Public on Feb 15 2019

city: Stockholm

first: Marcus

last: Buggert

state: PA

address: C2:94; Karolinska Universitetssjukhuset Huddinge

department: Microbiology

country: Sweden

institute: Karolinska Institutet

data_processing:
scRNA-seq: Data were initially filtered for quality. Paired-end sequencing reads were then trimmed to remove adaptor sequences and low-quality basecalls using the utility Trimmomatic. Reads were subsequently aligned using Bowtie against a genomic repeat element database derived from RepeatMasker software to quantify and remove transcript reads considered to be irrelevant for the analysis in hand (rRNA, rRNA, LINEs, SINEs, etc). The remaining reads were aligned against the most recent human genome build, hg38, using the splice-site aware aligner, STAR. As a bioinformatic measure of library quality, the total frequency of reads that could be mapped to the transcriptome was determined, and outliers were excluded from further analysis. Transcripts were then quantified and normalized using the bioinformatics package, Cufflinks. In our experience, a small number of libraries display low complexity and lack expression of highly expressed housekeeping genes. In most systems, a set of housekeeping genes should be expressed in every cell. We therefore use qPCR to identify viable samples expressing two distinct housekeeping genes. Samples with low or no expression of these genes are removed from Nextera library construction. To further ensure exclusion of data from single cells for which library construction was unsuccessful, we determined diversity (Shannon entropy and count of detected genes) using the R package, Vegan, and discarded outliers.
Analysis of TCR sequences were conducted through the software package, MiXCR, to assemble and annotate TCR sequences from the pool of reads which had not aligned to the reference genome in the previous step. After assembly, low quality and low frequency TCR chains were removed. Clonotypes were then built for each cell using the refined chain information. An average of 55 (range 23–143) TCRBV sequences were analyzed per patient.
Genome_build: mm10
Supplementary_files_format_and_content: EC_CD69_count.csv

source_name: CD69- CD8+ T cells

extract_protocol:
scRNA-seq: Single-cell analysis was derived from a previously published method (Shalek et al., Nature, 2014). Single HIV-tetramer+ cells were index sorted using a FACSAria II (BD Biosciences) directly into 96-well microtiter plates containing lysis buffer. In total, 552 cells were sorted. Cellular nucleic acids were recovered by processing the lysates with an RNEasy Plus Micro Kit (Qiagen) and then binding to RNAClean (SPRI) beads (Beckman Coulter). ERCC RNA control (Ambion) was diluted 1 in 107 from stock, and 10% by volume was added to the RNAClean beads prior to purification.
scRNA-seq: Libraries were prepared by getting mRNA be reverse transcribed from an anchored oligo-dT primer that includes a universal priming site at the 5’ end. RT reactions also included a template-switch oligonucleotide to allow the incorporation of the universal priming site at cDNA 3’ ends. Whole transcriptome cDNA was then amplified by PCR for 22–24 cycles using universal priming sites primers and Kapa HiFi Hot Start ReadyMix. After post-PCR clean-up, amplified whole transcriptome cDNA was incorporated into barcoded Illumina Nextera libraries and sequenced to a depth of about 2 million 150bp paired-end reads/cell on a HiSeq 4000 (Illumina).  and amplified for 14 PCR cycles. Libraries were pooled and paired-end sequenced (38bp+37bp).

tag: passages

value: FACS purified cells

value: mesenteric LN

value: CD69- CD8+ T cells


title: N722_S502_7: CD69neg scRNA-seq


title: Stages 3 to 6, Protocol x2, Stage 3 complete

value: in vitro differentiated pluripotent stem cell

value: SC-beta protocol x2


title: N722_S507_7: CD69neg scRNA-seq


title: N719_S503_7: CD69neg scRNA-seq


title: N718_S506_7: CD69neg scRNA-seq


title: N719_S510_7: CD69neg scRNA-seq


title: N718_S508_7: CD69neg scRNA-seq


title: N719_S502_7: CD69neg scRNA-seq


title: N718_S503_7: CD69neg scRNA-seq


title: N718_S502_7: CD69neg scRNA-seq


title: 1512_WGBS_Olig2

value: Brodmann Area 46 (BA46)

tag: age

value: Schizo


title: N720_S507_4: CD69neg scRNA-seq


title: N716_S505_7: CD69neg scRNA-seq


title: N719_S505_4: CD69neg scRNA-seq


title: N716_S506_7: CD69neg scRNA-seq


title: N722_S508_3: CD69neg scRNA-seq


title: N722_S505_3: CD69neg scRNA-seq


title: N722_S503_3: CD69neg scRNA-seq


title: N721_S511_3: CD69neg scRNA-seq


title: N722_S502_3: CD69neg scRNA-seq


title: N722_S506_3: CD69neg scRNA-seq


title: Stages 3 to 6, Protocol x1, Stage 4 complete

value: Stage 4


title: N721_S506_3: CD69neg scRNA-seq


title: N719_S506_3: CD69neg scRNA-seq


title: N720_S508_3: CD69neg scRNA-seq


title: N720_S510_3: CD69neg scRNA-seq


title: N721_S507_3: CD69neg scRNA-seq


title: N721_S503_3: CD69neg scRNA-seq


title: N721_S505_3: CD69neg scRNA-seq


title: N719_S505_3: CD69neg scRNA-seq


title: N718_S508_3: CD69neg scRNA-seq


title: N719_S503_3: CD69neg scRNA-seq


title: N718_S506_3: CD69neg scRNA-seq


title: N718_S505_3: CD69neg scRNA-seq


title: N718_S503_3: CD69neg scRNA-seq


title: N721_S510_3: CD69neg scRNA-seq


title: N716_S511_3: CD69neg scRNA-seq


title: N716_S508_3: CD69neg scRNA-seq


title: N721_S508_3: CD69neg scRNA-seq


title: N722_S508_2: CD69neg scRNA-seq


title: 1525_WGBS_NeuN

value: NeuN

value: F


title: N722_S506_2: CD69neg scRNA-seq


title: N722_S503_2: CD69neg scRNA-seq


title: N721_S511_2: CD69neg scRNA-seq


title: N722_S502_2: CD69neg scRNA-seq


title: N716_S505_3: CD69neg scRNA-seq


title: N721_S503_2: CD69neg scRNA-seq


title: N716_S503_3: CD69neg scRNA-seq


title: N718_S510_3: CD69neg scRNA-seq


title: N721_S502_2: CD69neg scRNA-seq


title: N720_S505_3: CD69neg scRNA-seq


title: N719_S510_2: CD69neg scRNA-seq


title: N720_S502_2: CD69neg scRNA-seq


title: N720_S508_2: CD69neg scRNA-seq


title: N719_S506_2: CD69neg scRNA-seq


title: N718_S507_3: CD69neg scRNA-seq


title: N720_S511_2: CD69neg scRNA-seq


title: N719_S503_2: CD69neg scRNA-seq


title: N718_S511_2: CD69neg scRNA-seq


title: N718_S502_2: CD69neg scRNA-seq


title: N718_S507_2: CD69neg scRNA-seq


title: N719_S502_2: CD69neg scRNA-seq


title: N716_S502_2: CD69neg scRNA-seq


title: N718_S505_2: CD69neg scRNA-seq


title: N722_S508_7: CD69pos scRNA-seq

source_name: CD69+ CD8+ T cells

value: CD69+ CD8+ T cells


title: N722_S506_7: CD69pos scRNA-seq


title: N716_S508_2: CD69neg scRNA-seq


title: N721_S506_7: CD69pos scRNA-seq


title: N722_S503_7: CD69pos scRNA-seq


title: N716_S511_2: CD69neg scRNA-seq


title: N721_S505_7: CD69pos scRNA-seq


title: N720_S503_7: CD69pos scRNA-seq


title: N721_S503_7: CD69pos scRNA-seq


title: N720_S507_7: CD69pos scRNA-seq


title: N721_S502_7: CD69pos scRNA-seq


title: N720_S506_2: CD69neg scRNA-seq


title: N720_S502_7: CD69pos scRNA-seq


title: N719_S506_7: CD69pos scRNA-seq


title: N719_S505_7: CD69pos scRNA-seq


title: N718_S511_7: CD69pos scRNA-seq


title: N719_S508_7: CD69pos scRNA-seq


title: N718_S505_7: CD69pos scRNA-seq


title: N718_S510_7: CD69pos scRNA-seq


title: N716_S511_7: CD69pos scRNA-seq


title: N718_S507_7: CD69pos scRNA-seq


title: N716_S503_7: CD69pos scRNA-seq


title: N716_S502_7: CD69pos scRNA-seq


title: N716_S508_7: CD69pos scRNA-seq


title: N721_S508_4: CD69pos scRNA-seq


title: N722_S507_4: CD69pos scRNA-seq


title: N721_S510_2: CD69neg scRNA-seq


title: N721_S505_4: CD69pos scRNA-seq


title: N720_S503_4: CD69pos scRNA-seq


title: N720_S511_3: CD69pos scRNA-seq


title: N718_S508_4: CD69pos scRNA-seq


title: N718_S505_4: CD69pos scRNA-seq


title: N722_S507_3: CD69pos scRNA-seq


title: N716_S510_3: CD69pos scRNA-seq


title: N719_S507_3: CD69pos scRNA-seq


title: N721_S502_3: CD69pos scRNA-seq


title: N718_S511_3: CD69pos scRNA-seq


title: N720_S503_3: CD69pos scRNA-seq


title: N720_S506_3: CD69pos scRNA-seq


title: N721_S508_2: CD69pos scRNA-seq


title: N722_S505_2: CD69pos scRNA-seq


title: N719_S508_3: CD69pos scRNA-seq


title: N721_S506_2: CD69pos scRNA-seq


title: N720_S507_3: CD69pos scRNA-seq


title: N720_S510_2: CD69pos scRNA-seq


title: N721_S507_2: CD69pos scRNA-seq


title: N721_S505_2: CD69pos scRNA-seq


title: N722_S507_2: CD69pos scRNA-seq


title: N719_S511_2: CD69pos scRNA-seq


title: N720_S505_2: CD69pos scRNA-seq


title: N720_S503_2: CD69pos scRNA-seq


title: N720_S507_2: CD69pos scRNA-seq


title: N719_S511_3: CD69pos scRNA-seq


title: N716_S510_2: CD69pos scRNA-seq


title: N718_S506_2: CD69pos scRNA-seq


title: LN naïve: DP ATAC-seq Rep 1

data_processing:
ATAC-seq: Quality assessment of raw reads was achieved with FastQC and contaminants were removed using Trimgalore. Human (GRCh37) reference genome was downloaded from UCSC repository Reads and samples were subsequently aligned using Bowtie. De novo motif analysis was performed on the top and bottom 100 enhancers using Homer. The top/bottom 100 enhancers were also linked to genes based on proximity (<10kbp) in order to enable GO term enrichment analysis using the GSEA website and volcano plot visualization between CD69+ and CD69- CD8+ T cells. Visualization of ATAC-seq tracks (peaks) was conducted using Integrative genomics viewer (igv) version 2.3.93.
Genome_build: mm10

source_name: naïve CD8+ T cells

extract_protocol:
ATAC-seq: ATAC-seq was performed as previously described with minor modifications (Buenrostro et al., Nature Methods, 2013). Fifty thousand cells from FACS or from cultur were pelleted at 550 x g and washed with 1 mL 1x PBS followed by lysis with 50 μL lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Accessible chromatin was tagmented with Tn5 transposase (FC-121-1030; Illumina) for 45-75 minutes depending on the cell-type in a 37°C waterbath.
ATAC-seq: Tagmented DNA was amplified for 12 cycles of PCR, purified, and the prepared libraries were paired-end sequenced (38bp+37bp).

value: hepatic lymph node

value: naive CD8+ T cells


title: LN CD69-: DP ATAC-seq Rep 2


title: LN naïve: DP ATAC-seq Rep 2


title: LN CD69+: DP ATAC-seq Rep 1


title: LN CD69+: DP ATAC-seq Rep 2


title: LN CD69-: DP ATAC-seq Rep 1


title: C9: LN3 CD69- RNA-seq

data_processing:
RNA-seq: Fastq files from three sequencing runs were concatenated and aligned using STAR 2.5.2a and hg38 to generate a final unique paired mapped read depth ranging from 8 million to 13.6 million reads per sample. The aligned files were normalized using Deseq2.
Genome_build: mm10

source_name: CD8+ T cells

extract_protocol:
RNA-seq: 250 cells per subset were sorted using a FACSAriaII (BD Biosciences) directly into lysis buffer provided with the SMART-Seq v4 Ultra Low Input RNA Kit (Takara) and snap frozen.
RNA-seq:  RNA-seq libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara) according to manufacturer’s protocols. Briefly, 3’ SMART-Seq CDS (oligo-dt) Primers were hybridized to the poly(A) tail of all the mRNA and reverse transcribed with the SMARTScribe RT enzyme. cDNA was pre-amplified using SeqAmp DNA polymerase and frozen. Amplified material was purified using Agencourt AMPure XP beads (Beckman) and cDNA quantity was assessed on a Qubit 3.0 (Thermo) and fragment size was evaluated on a 2100 BioAnalyzer (Agilent). The PCR products were next indexed using the Nextera XT DNA Library Prep Kit (Illumina) according to manufacturer’s protocol. Briefly, products were tagmented using the Amplicon tagment mix, containing Tn5 transposase, and indexed using Nextera index 1 (i7) and index 2 (i5) primers. The libraries were again cleaned-up with Agencourt AMPure XP beads, pooled, quantified and sequenced across 75 base pairs (bp) using a paired-end strategy with a 150-cycle high output flow cell on a NextSeq 550 (Illumina).

value: mesenteric lymph node

value: CD8+ T cells


title: C8: LN3 CD69+ RNA-seq


title: B9: LN2 CD69- RNA-seq


title: A9: LN1 CD69- RNA-seq


title: A8: LN1 CD69+ RNA-seq


title: Sample13_F_7

status: Public on Feb 14 2019

city: Los Angeles

first: Ye

middle: Emily

last: Wu

state: CA

address: 635 Charles E. Young Dr. South

institute: UCLA

description: Cells from naïve female mice.

data_processing:
Demultiplexing was performed with bcl2fastq2 v2.17.1.14
Cell barcodes and UMI were extracted using Drop-seq_tools v1.12
Read 2 was aligned with STAR v2.5.0a
Each aligned read was tagged with its mate-pair UMI and cell barcode
Each aligned exonic read was tagged with a gene name.
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell
44,437 cells with > 200 genes, > 250 transcripts, and a read number/transcript number ratio > 3.5 were used for the major cell type clustering analysis in the associated publication. Raw UMI counts for 16,961 genes detected in > 20 cells with > 30 transcripts were retained. rRNA, tRNA, and mitochondrial RNA genes were removed.
PCA, tSNE, and Louvain-Jaccard clustering were performed to identify major cell types
Clusters that likely arised from doublets were removed. The remaining 43,388 cells were merged into a single matrix (MeA_AllCells_DGE.csv).
Genome_build: mm10
Supplementary_files_format_and_content: flat text files with tab delimiters; digital gene expression matrices of raw UMI counts for each gene in each cell; cells in columns and genes in rows; cells named as X_Y_Z  or X_Y where X is cell barcode, Y is sample name, and Z is major cell type.

source_name: Medial amygdala

growth_protocol: Mice were housed with a reverse light cycle (12 hr light/12 hr dark) and ad libitum access to food and water.

extract_protocol:
Single-cell suspensions were generated using the Act-Seq protocol, and processed through Drop-Seq to produce single-cell cDNA libraries attached to microbeads. cDNAs were amplified by PCR and prepared for sequencing through tagmentation.
Sequencing libraries were generated through tagmentation using Illumina Nextera XT DNA Library Prep Kit.

treatment_protocol: Mice were single-housed for at least one day before single-cell dissociation. No other treatments.

value: Medial amygdala

value: 9 weeks

value: Female


title: Combined Treg populations

status: Public on Dec 31 2018

city: MInneapolis

first: Michael

last: Farrar

state: MN

address: 2101 6th Street SE

department: Lab Medicine and Pathology

institute: University of Minnesota

description:
combined sorted populations: CD25+Foxp3-, CD25-Foxp3lo, CD25+Foxp3+
Treg_population_single_library.txt.gz

data_processing:
CellRanger pipeline was used to demultiplex, map and retrieve counts for all of the samples. CellRanger version 1.3.1 was used for the single-library combined population and was mapped to mm10 reference genome.
CellRanger version 2.0 was used for the sorted populations and mapped to mm10 with the GFP sequence construct added as a new chromosome (GFP-SV40PA.1) to detect Foxp3 expression. Both version of the mm10 were filtered for protein coding genes only.
Sorted populations prepared as separate libraries were sequenced in separate lanes. Populations were then aggregated together using the CellRanger aggr command.
Analysis of sequencing data was performed using the Seurat package (R package version 1.4.0.12).
For the data where all of the sorted populations were combined and processed in 1 library, data was filtered to keep all genes expressed in >=5 cells and keep all cells with >=200 and <= 2000 genes expressed.
For the sorted populations that were aggregated together, data was filtered to keep all genes expressed in >=5 cells and keep all cells with >=100 and <=2500 genes expressed.
The global-scaling normalization method “LogNormalize” normalizes the gene expression measurements for each cell by the total expression, multiplies this by a scale factor (10,000), and log-transforms the result.
Each sorted population in the aggregated data is represented as either an -1, -2, or -3 (after the UMI sequence for each cell).
For the rep1 data, -1 depicts the CD25posFoxp3neg population, -2 depicts the CD25negFoxp3lo population and -3 depicts the CD25posFoxp3pos population.
For the rep2 data, -1 depicts the CD25negFoxp3lo population, -2 depicts the CD25posFoxp3neg population and -3 depicts the CD25posFoxp3pos population.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Seurat global-scaling normalization method “LogNormalize”

source_name: Thymic T cells

extract_protocol:
A single cell suspension was generated from the thymus then magnetically depleted for CD8/Ter119 before sorting CD25+Foxp3-, CD25-Foxp3lo and CD25+Foxp3+ cells from CD4+CD73- thymocytes on a BD Aria II
Cells were resuspended at 1x10^6/mL in 1xPBS + 50%FBS and mixed in equal ratios before capture via 10X Genomics Chromium platform (ChromiumTM Single cell 3' v2 chemstry)

value: C57BL/6 female FOXP3-GFP

value: 48 day

tag: genotype

value: IRES-GFP with SV40 polyA cassestte knocked into the 3'UTR of the Foxp3


title: N719_S508_2: CD69pos scRNA-seq

value: FACS purified cells

value: mesenteric LN


title: CD25negFoxp3lo rep2

description:
Contains CD25-Foxp3lo population
Combined_sorted_Treg_populations_rep2.txt.gz

value: 49 day


title: CD25posFoxp3neg rep2

description:
Contains CD25+Foxp3- population
Combined_sorted_Treg_populations_rep2.txt.gz


title: CD25posFoxp3pos rep1

description:
Contains CD25+Foxp3+ population
Combined_sorted_Treg_populations_rep1.txt.gz

value: 51 day


title: CD25posFoxp3pos rep2

description:
Contains CD25+Foxp3+ population
Combined_sorted_Treg_populations_rep2.txt.gz


title: B8: LN2 CD69+ RNA-seq


title: N716_S505_2: CD69pos scRNA-seq


title: CD25posFoxp3neg rep1

description:
Contains CD25+Foxp3- population
Combined_sorted_Treg_populations_rep1.txt.gz


title: D60_3X130_T1_20180208

status: Public on Dec 07 2018

city: Baltimore

first: Suvarna

last: Nadendla

state: MD

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

data_processing:
Neisseria gonorrhoeae: Sequence reads were trimmed for adaptor sequence and mapped to the Opaless_3X or H041  Neisseria genomes using bowtie v1.0 with parameters -mode=v --num_mismatches=2 --file-type=fastq --seedlen=28 --minins=0 --maxins=600 --library-type=fr  --args='--sam' --v --gzip
Homo sapiens: Sequenced reads were trimmedfor adaptor sequence and mapped to the 2018 GRCh38 Human genome assembly using HISAT v2.0 with parameters -mismatch-penalties=6,2 --softclip-penalties=2,1 --read-gap-penalties=5,3 --ref-gap-penalties=5,3 --min-intronlen=20 --max-intronlen=500000 --score-min=L,0,-0.2 --pen-cansplice=0 --num-threads=1 --pen-noncansplice=12 --pen-canintronlen=G,-8,1 --pen-noncanintronlen=G,-8,1 --rna-strandness=RF --dta-cufflinks=1 --num-alignments=5 --minins=0 --maxins=600 --no-unal=1 --args='' --v
Neisseria gonorrhoeae: Reads Per Kilobase per Million values for gene features were calculated as described in Shenoy et al. PLoS Pathog. 2017 Aug 25;13(8):e1006582. doi: 10.1371/journal.ppat.1006582. eCollection 2017 Aug.
Homo sapiens: Reads Per Kilobase per Million values for exon features were calculated as described in Shenoy et al. PLoS Pathog. 2017 Aug 25;13(8):e1006582. doi: 10.1371/journal.ppat.1006582. eCollection 2017 Aug.
Genome_build: All data derived from the Opaless and Opaless_3X strains have been mapped to the Opaless_3X genome (GenBank Accession: WHPL00000000), while data derived from the H041 strain have been mapped to the H041 genome (GenBank Accession: WHPH00000000). All human data were mapped to 2018 GRCh38 Human genome assembly.

organism: Neisseria gonorrhoeae

source_name: Neisseria gonorrhoeae strains FA1090/H041 and adherent primary human neutrophils, alone and after co-culture over time

growth_protocol: N. gonorrhoeae of strain FA1090 or H041/WHOX (Ohnishi et al, Emerg Infect Dis 2011) was grown in GCBL medium containing Kellogg's supplements and sodium bicarbonate for successive rounds of growth in order to enrich for exponentially growing bacteria, as described in Criss AK et al, Cellular Microbiology 2009. FA1090 N. gonorrhoeae were constitutively piliated and deleted for Opa proteins ("Opaless" or 130; Ball and Criss, J Bacteriol 2013). 130 was sequentially transformed with the penA, mtrR, and penB alleles from superbug strain H041 to generate the isogenic antibiotic resistant strain "3X 130". Primary human neutrophils were isolated from the venous blood of healthy human donors by dextran sedimentation followed by Ficoll purification and hypotonic lysis of residual erythrocytes. Neutrophils were placed on tissue culture treated plastic coverslips in RPMI medium containing 10% fetal bovine serum and 10 nM interleukin-8 for 30 minutes to allow for adherence.

extract_protocol:
At indicated times, samples were placed on ice. Bacteria alone were collected into microcentrifuge tubes, pelleted, and stored in RNAprotect at -80C. Supernatants were discarded from neutrophil containing samples, RNA protect was added, and samples were stored at -80C. Samples were exposed to EDTA pre-extraction and during the lysis step. Extractions were performed using Qiagen’s RNeasy extraction kit as per manufacturer’s protocol. An additional Turbo DNase was performed after the final step of RNeasy protocol. Quality and quantity were determined using the Agilent 4200 TapeStation System.
Strand specific RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: N. gonorrhoeae was left untreated or exposed to sublethal concentrations of ceftriaxone (0.25 ng/ml for 130, 31.25 ng/ml for 3x130, 62.5 ng/ml for H041), gentamicin (156 ng/ml for 130 and H041, 312.5 ng/ml for 3x130), or azithromycin (6 ng/ml for 130 and H041, 12.5 ng/ml for 3x130) for 1 hour. Bacteria were then added to adherent human neutrophils at MOI = 1 in RPMI + 10% FBS, or inoculated into RPMI + 10% FBS without neutrophils. Incubations were for 0 hour or 1 hour. Antibiotics were kept at the same concentration throughout the experiment.

tag: donor

tag: treatment condition

value: Bacteria alone

tag: human cell type

tag: incubation time

value: 60 min medium alone

tag: n. gonorrhoeae strain


title: D60_H041_T1_20180208


title: D6_H041_T1_20180131


title: D55_130_T1_20180201

value: Opaless


title: D55_H041_T1_20180201


title: D55_3X130_T1_20180201


title: D5_130_T1_20180206

description: Total RNAs extracted from PMNs from this donor D5 were of lower quality (lower RNA integrity [RIN] values), affecting overall RNA-seq data quality


title: D5_3X130_T1_20180206


title: D5_H041_T1_20180206


title: D60_PMN_H041_T1_20180208

organism:
Neisseria gonorrhoeae
Homo sapiens

value: Co-culture

value: PMN

value: 60 min medium with PMN


title: D60_PMN_130_T1_20180208


title: D60_PMN_H041_T0_20180208

value: 0 min medium with PMN


title: D60_PMN_3X130_T1_20180208


title: D6_130_T1_20180131


title: CD25negFoxp3lo rep1

description:
Contains CD25-Foxp3lo population
Combined_sorted_Treg_populations_rep1.txt.gz

tag: strain


title: D60_130_T1_20180208


title: D60_PMN_130_T0_20180208


title: D6_PMN_H041_T0_20180131


title: D31_130_T1_20180323

description: Total RNAs extracted from PMNs from this donor D31 were of lower quality (lower RNA integrity [RIN] values), affecting overall RNA-seq data quality


title: D6_PMN_130_T1_20180131


title: D55_PMN_3x130_T1_20180201


title: D6_PMN_H041_T1_20180131


title: D55_PMN_3x130_T0_20180201


title: D55_PMN_130_T0_20180201


title: D55_PMN_H041_T0_20180201


title: D55_PMN_H041_T1_20180201


title: D5_PMN_3X130_T1_20180206


title: D55_PMN_130_T1_20180201


title: D5_PMN_H041_T1_20180206


title: D5_PMN_130_T1_20180206


title: D5_PMN_3X130_T0_20180206


title: D5_PMN_130_T0_20180206


title: D60_PMN_3X130_T0_20180208


title: D31_PMN_H041_T0_20180323


title: D31_PMN_H041_T1_20180323


title: D31_3X130_T1_20180323


title: D31_PMN_130_T0_20180323


title: D31_PMN_3X130_T0_20180323


title: D31_PMN_130_T1_20180323


title: D31_PMN_3X130_T1_20180323


title: Sample_21; REGN1193 (10 mg/kg); HFD

status: Public on Nov 09 2018

city: Tarrytown

first: Haruka

last: Okamoto

address: 777 Old Saw Mill River Rd

institute: Regeneron

description: Effects of GCGR mAb on ALT/AST in DIO mice

data_processing:
Illumina bcl2fastq v2.17 used to convert BCL to fastq
Reads were decoded based on their barcodes. Read quality was evaluated using FastQC.
Reads were mapped to the reference genome (mouse: GRCm38) using using ArrayStudio® software (OmicSoft®, Cary, NC) allowing two mismatches.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Liver

extract_protocol: Strand-specific RNA-seq libraries were prepared using KAPA mRNA-Seq Library Preparation Kit (Kapa Biosystems). Twelve-cycle PCR was performed to amplify libraries. Sequencing was performed on Illumina HiSeq®2500 (Illumina) by multiplexed single-read run with 33 cycles.

value: Liver

tag: treatment

tag: diet

value: HFD

tag: gender

value: male


title: Sample_22; REGN1193 (10 mg/kg); HFD


title: Sample_19; REGN1193 (10 mg/kg); HFD


title: D5_PMN_H041_T0_20180206


title: Sample_20; REGN1193 (10 mg/kg); HFD


title: Sample_12; REGN496 (10 mg/kg); HFD

value: REGN496 (10 mg/kg)


title: Sample_18; REGN1193 (10 mg/kg); HFD


title: Sample_17; REGN496 (10 mg/kg); HFD


title: Sample_23; REGN1193 (10 mg/kg); HFD


title: Sample_14; REGN496 (10 mg/kg); HFD


title: Sample_15; REGN496 (10 mg/kg); HFD


title: Sample_13; REGN496 (10 mg/kg); HFD


title: Sample_11; REGN1193 (10 mg/kg); Chow

value: Chow


title: Sample_10; REGN1193 (10 mg/kg); Chow


title: Sample_8; REGN1193 (10 mg/kg); Chow


title: Sample_7; REGN1193 (10 mg/kg); Chow


title: Sample_9; REGN1193 (10 mg/kg); Chow


title: Sample_6; REGN1193 (10 mg/kg); Chow


title: Sample_5; REGN496 (10 mg/kg); Chow


title: Sample_4; REGN496 (10 mg/kg); Chow


title: Sample_3; REGN496 (10 mg/kg); Chow


title: Sample_2; REGN496 (10 mg/kg); Chow


title: Sample_1; REGN496 (10 mg/kg); Chow


title: A549 shCtl, biological rep1 (WA1)

status: Public on Nov 20 2018

city: Gainesville

first: Lizi

state: FL

address: 2033 Mowry Road

institute: University of Florida

description: Gene expression data

hyb_protocol: Following fragmentation, sscDNA were hybridized for 16 hr at 45C on Affymetrix Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner

data_processing: The data were normalized using RMA normalization approach with Affymetrix Expression Console.

source_name: human lung carcinoma epithelial cells, vector control

label_protocol: Biotinylated sscDNA were prepared according to the standard Affymetrix protocol from total RNA.

growth_protocol: Cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% inactivated fetal bovine serum and 1% penicillin/streptomycin at 37°C under 5% CO2.

extract_protocol: Total RNAs were extracted from cells using the TRIzol Reagent and purified by RNeasy kit followed by on-column DNase digestion.

treatment_protocol: shCtl: control, and shINSL4 (INSL4 shRNA, knockdown)

tag: cell line

value: A549 cells

tag: genotype/variation

value: vector knock-down control


title: Sample_16; REGN496 (10 mg/kg); HFD


title: A549 shCtl, biological rep2 (WB1)

description: Gene expression data


title: A549 shINSL4 A, biological rep1 (WA2)

description: Gene expression data

source_name: human lung carcinoma epithelial cells, INSL4 knock-down

value: INSL4 knock-down


title: A549 shINSL4 A, biological rep2 (WB2)

description: Gene expression data


title: RTR1 deletion Rpb3-FLAG ChIP-exo prep 1

status: Public on Sep 25 2018

city: Indianapolis

first: Yunlong

last: Liu

state: IN

address: 410 West 10th Street

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

data_processing:
For the ChIP-exo data,  sequence reads were aligned with BFAST (v.0.7.0a) to the reference genome.
For ChIP-exo data , aligned reads were fitered with NGSUtils (Breese and Liu, Bioinformatics 2013), only unique mapped reads with no more than 2 mismatchs were kept.

For the ChIP-exo data, RPKM normalized bigWig files were generated with deepTools.
Genome_build: sacCer3
Supplementary_files_format_and_content:  ChIP-exo: bigWig files

source_name: Saccharomyces cerevisiae

growth_protocol: All cells were grown to an OD600 of 0.8

extract_protocol:
ChIP-exo
ChIP-exo protocol


title: RTR1 deletion Rpb3-FLAG ChIP-exo prep 2


title: WT Rpb3-FLAG ChIP-exo prep 2

value: wild type


title: WT Rpb3-FLAG ChIP-exo prep 1


title: Bulk_9 (C6)

status: Public on Jun 16 2018

first: Richard

middle: Sungho

last: Ahn

address: 611 Charles E. Young Drive East, UCLA, Boyer Hall, 510C

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California Los Angeles

description: FPKM-table-all-samples_FACS-seq-project.csv

data_processing:
Read quality was checked using FastQC v. 0.11.4
Reads with adapter contamination were trimmed using Trimmomatic v. 0.32
Reads aligned using STAR vs. 2.4.2a
FPKMs and differential expression tests calculated using the Cufflinks Suite v. 2.2.1.
Gene annotations obtained from RefSeq
Genome_build: hg19
Supplementary_files_format_and_content: CSV file containing a matrix of FPKM values for all samples.

source_name: Bulk controls (Normal Skin)

extract_protocol:
RNA was extracted from biopsy samples using the Qiagen Allprep DNA/RNA mini kit.
The Ovation RNA-seq System V2 protocol was implemented to amplify cDNA from 500 pg of qualified mRNA from each sample. cDNA amplification was performed using NuGEN Ribo-SPIA technology. The cDNA was then sheared as ~200 bp fragments, end-repaired, followed by A-tailing and adapter ligation reactions. The library was PCR enriched and purified using the Ampure XP bead size selection method.

value: skin

tag: subject status

value: healthy control


title: Bulk_10 (C5)

tag: tissue


title: HCASMC scrambled siRNA_S18

status: Public on Sep 11 2018

city: Stanford

first: Thomas

last: Quertermous

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

data_processing:
Reads were processed using rnaSeqFPro, a workflow for full processing of RNASeq data starting from fastq files. In brief, the quality control was performed using FastQC, mapping to the human genome hg19 was performed using STAR second pass mapping to increase the percentage of mapped reads, and counting was done with featureCounts using GENCODE gtf annotation. Next, rnaSeqFPro performed differential analysis using DESeq2, conducted principal component analysis and hierarchical clustering using standard R functions, plotPCA and heatmap.2 and generated graphs using gglot2. DESeq2 gave 493 differentially expressed (DE) genes (FDR £ 0.05).
Genome_build: hg19
Supplementary_files_format_and_content: text file with raw counts.

source_name: Cultured coronary artery smooth muscle cells

growth_protocol: Primary human coronary artery smooth muscle cells (HCASMCs) were purchased from three different manufacturers, PromoCell, Lonza and Cell Applications at passage 2 and were cultured in smooth muscle cell basal media along with hEGF, insulin, hFGF-B and fetal bovine serum (FBS) (Lonza # CC-3182) according to the manufacturer’s instructions. HCASMCs between passages 5-8 were used for all the experiments.

extract_protocol:
RNA for all samples was extracted using the RNAeasy mini kit (Qiagen). HCASMC RNA (500 ng) were reverse transcribed using the High capacity RNA-to-cDNA Synthesis kit (Applied Biosystems).
Three experimental and three control samples were generated, RNA was converted to cDNA library as per workflow at Novogene, and sequenced on a HiSeq 4000 machine, 125 bp paired end reads.

treatment_protocol: SMAD3 (s8401 and s8402) silencer select siRNAs were purchased from Life Technologies. siRNA transfection was performed using Lipofectamine RNAiMAX (Life Technologies). For each well treated with the SMAD3 siRNA or scrambled control (Life technologies, #4390843), the final concentration was 20 nM. HCASMCs were seeded in 6 well plates and grown to 75% confluence before siRNA transfection. HCASMCs were transfected with the SMAD3 siRNA or scrambled control for 12 hours and subsequently collected and processed for RNA isolation after 48 hrs of transfection using the RNeasy kit (Qiagen).

tag: cell type

value: coronary artery smooth muscle cells

tag: culture method

value: Grown in serum

tag: knockdown

value: scrambled siRNA


title: Bulk_8 (C2)


title: WT Nrd1-TAP ChIP-exo prep 1

tag: genotype


title: HCASMC scrambled siRNA_S17


title: D6_PMN_130_T0_20180131

tag: donor

value: Co-culture

value: PMN

value: Opaless


title: Bulk_13 (107)


title: RTR1 deletion Nrd1-TAP ChIP-exo prep 2


title: Bulk_6 (C8)


title: RTR1 deletion Nrd1-TAP ChIP-exo prep 1


title: Bulk_5 (C15)


title: Bulk_3 (C11)


title: Bulk_1 (C13)


title: WT Nrd1-TAP ChIP-exo prep 2


title: Teff_6

source_name: CD4+ T effectors

value: CD4+ T effector


title: Teff_7


title: Teff_9


title: Teff_5


title: Teff_8


title: Bulk_11 (C4)


title: Bulk_12 (V008)


title: Teff_4


title: HCASMC scrambled siRNA_S19


title: Teff_3


title: Teff_2


title: Teff_10


title: Bulk_7 (C3)


title: KC_8

source_name: Keratinocytes

value: Keratinocyte


title: KC_7


title: KC_9


title: Bulk_4 (C10)


title: KC_6


title: KC_4


title: KC_3


title: KC_2


title: KC_1


title: Bulk_2 (C12)


title: KC_11


title: KC_10


title: DC_8

source_name: Dendritic cells

value: Dendritic cell


title: DC_9


title: DC_6


title: DC_5


title: DC_4


title: DC_3


title: CD8_8

value: CD8+ T cell


title: DC_1


title: DC_10


title: CD8_6


title: CD8_7


title: CD8_5


title: CD8_4


title: CD8_1


title: Control-24048

status: Public on Jan 01 2018

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: Lavage-based self-sample

data_processing:
Each library was indexed in order to multiplex up to 5 samples per sequencing run.
Sequenced reads were analyzed using the miRDeep2 algorithm (Friedländer et al., 2012 Nucl Acids Res). In brief, reads were trimmed for adaptor sequences, and filtered for low-quality sequences and sequences shorter than 18 nucleotides followed by alignment to the human genome (hg19). Input from known miRNAs was obtained from miRBase version 20 (Kozomara et al., 2011, Nucl Acids Res). To avoid multiple counting of miRNA sequences that can originate from several genomic loci, we only counted the expression of miRNA paralogs once.
miRNA read counts were normalized according to the trimmed mean of M values (TMM) normalization strategy (Robinson et al., 2010 Genome Biol). Subsequently, the distribution of miRNA read counts was assessed and samples that depicted an atypical distribution were excluded.
Normalized miRNA read counts were square-root transformed to the quasi Gaussian scale followed by miRNA data standardization. Only those miRNAs that exhibited non-zero read counts in at least 3 samples were included.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include microRNA names and standardized count values for each sample

source_name: Self-sample HPV-positive control_24048

extract_protocol:
Total RNA from self-samples was extracted using Direct-ZolTM RNA Miniprep (Zymo Research, Freiburg, Germany) following the manufacturer's instructions
Preparation of cDNA libraries was performed with equal amount of input RNA per sample (1000ng of total RNA) using the TruSeq Small RNA Sample Preparation Kit according to the manufacturer's instruction (Illumina, San Diego, CA, USA)

tag: histology

value: normal


title: CD8_3


title: CD8_2


title: KC_5


title: Control-23558

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_23558


title: Control-23165

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_23165


title: Control-21810

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_21810


title: Control-22768

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_22768


title: Control-22260

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_22260


title: Control-21765

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_21765


title: Control-21967

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_21967


title: Control-21586

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_21586


title: DC_7


title: Control-21398

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_21398


title: DC_2


title: Control-21342

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_21342


title: Control-21808

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_21808


title: Control-21014

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_21014


title: aSTAT4_STAT4KO_STIM_3_CHIP

status: Public on Dec 20 2017

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

data_processing:
BCL files were converted to fastq using bcl2fastq (v1.8.3 and v1.8.4)
ChIP-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36) and aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Peak-calling was done on concordantly aligned paired reads using MACS2 (2.1.1.20160309).
BigWig files were generated by converting BAM files to size-normalized BEDGRAPH files using bedtools (v2.26.0) and converted to bigWig using UCSC's bedGraphToBigWig (v4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files normalized by size factors calculated by DESeq2 among all ChIP (non-input) samples in peak regions or flank regions (see manuscript)

source_name: splenic NK cells

extract_protocol:
Protein was cross-linked to DNA with 0.75% formaldehyde. Clarified supernatant from sonicated nuclei were applied to antibody-bound beads. After de-crosslinking and elution, DNA was isolated using Qiagen Gel Extraction Kit. Input samples were clarified supernatant that were not applied to antibody-bound beads.
Immunoprecipitated DNA was quantified by Picogreen and size was evaluated on a HighSense BioAnalyzer chip. When possible, fragments between 100 and 600 bp were size selected and Illumina Hiseq libraries were prepared using the Kapa DNA library preparation chemistry (Kapa Biosystems) using 12-15 cycles of PCR. Adaptors were diluted 1/10 or  1/50 depending on the starting amount of material available. Barcoded libraries were run on Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina). An average of 57 million paired reads were generated per sample.

tag: chip antibody

value: anti-STAT4 (Santa Cruz, sc-486, clone C-20, lot# c2114)

tag: condition

value: splenic NK cells


title: Control-20677

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_20677


title: aSTAT4_STAT4WT_STIM_2_CHIP


title: miCLIP_NSUN6_HEK293_rep2

status: Public on Feb 14 2017

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

data_processing:
For miCLIP analysis, miCLIP reads were mapped to the human reference genome (hg19/GRCh37) by using bowtie with parameters –m 1 –v 1 to select uniquely mapping reads allowing one mismatch.
Genome_build: hg19
Supplementary_files_format_and_content: bed file with genome-wide RNA methylation levels (available on the series record), bedfiles with miCLIP stop positions

source_name: Embryonic kidney cells

extract_protocol:
For miCLIP, myc-tagged NSUN3 or NSun6 constructs were transfected into HEK293 cells which were harvested 24 hours post-transfection. Cells were then lysed in lysis buffer and treated with high concentration of DNase and low concentration of RNaseI to partially fragment RNAs. Lysates were incubated with proteinG dynabeads in the presence of anti-myc antibody to isolate NSUN-RNA complexes.  Libraries were then prepared following isolation of RNAs from the protein-RNA complexes.
Libraries were prepared using Illumina TruSeq RNA prep kits

tag: antibody

value: anti c-myc 9E10

tag: antibody manufacturer

value: Sigma; catalog number M4439


title: aSTAT4_STAT4WT_STIM_1_CHIP


title: aSTAT4_STAT4WT_STIM_3_CHIP


title: miCLIP_NSUN6_HEK293_rep3


title: miCLIP_NSUN6_HEK293_rep1


title: eHDAC6-Guide2-Rep3

status: Public on Nov 11 2016

first: Jesse

last: Engreitz

address: 240 Pasteur Drive

data_processing:
Filter out reads aligning to abundant RNAs (rRNA, tRNA, snRNA, etc.) using bowtie2-2.1.0 - see hg19_abundant_rnas.fa supplementary file
Align to hg19 with Tophat-2.0.8 using their provided gene annotations
Remove duplicate reads with Picard
Remove reads with MAPQ < 30 with Samtools-0.1.19
Genome_build: hg19
Supplementary_files_format_and_content: counts.txt is a tab-delimited file conataining the number of sequencing reads aligning to exonic sequence of each gene - see hg19_refseq_annotation.bed supplementary file

growth_protocol: K562 cells expressing catalytically-dead Cas9 fused to a KRAB repressive domain from a doxycycline-inducible promoter were grown in RPMI with 10% FBS.

extract_protocol:
Ten thousand cells were lysed in RLT and RNA was extracted with the Qiagen Rneasy Kit
Custom strand-specific RNA-Sequencing (see Engreitz et al 2013)

treatment_protocol: Cells were transduced with the listed sgRNA and induced for 24 hours with doxycycline

tag: cell line/type

tag: tranduced with

value: eHDAC6-Guide2 sgRNA

tag: targetted element

tag: induced with

value: doxycycline for 24hrs


title: eHDAC6-Guide1-Rep3

tag: genotype/variation

value: expressing catalytically-dead Cas9 fused to a KRAB repressive domain from a doxycycline-inducible promoter

value: eHDAC6-Guide1 sgRNA


title: eHDAC6-Guide1-Rep2


title: eHDAC6-Guide1-Rep1


title: eHDAC6-Guide2-Rep1